Vertices not aligning
This problem shouldn't harm your model in anyway, but if you want to fix it you should do the following:

Click on the drop-down next to the magnet, hot-key = Control + Shift + Tab:

Select the following options: Increment, Scale. It doesn't matter if you have selected Move and/or Rotate:


Click the magnet to activate snapping, hot-key = Shift + Tab. I don't have a picture for this, if you need it you can tell me. Instead of clicking the magnet, you can also hold Control while scaling.